Realigning Clinical Studies from HG38 to T2T-CHM13 to Discover Differences Between Using Different Reference Genomes

Realigning Clinical Studies from HG38 to T2T-CHM13 to Discover Differences Between Using Different Reference Genomes | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Realigning Clinical Studies from HG38 to T2T-CHM13 to Discover Differences Between Using Different Reference Genomes Nikhil Sharma This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7643242/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract In genomics research, reference genomes are used by researchers to compare sequencing data. Human reference genomes represent the complete set of DNA within a cell. The first human reference genome was released in 2003, though incomplete due to technological barriers. In December of 2013, the HG38 genome, an updated version of previous genomes, was released, and it currently remains the most used reference genome due to its abundant annotations. Later in 2022, T2T-CHM13 was released, representing the first complete Human reference genome assembly, but most groups still use the HG38 genome. I hypothesize that using the T2T-CHM13 human reference genome for alignments will display more mapped reads, as the T2T-CHM13 is complete and, therefore, contains sections of the genome that older reference genomes, such as the HG38 reference genome, lack. In this study I realigned publicly available Renal Carcinoma cell line RNA-sequencing data, from the Cancer Cell Line Encyclopedia, to the T2T-CHM13 genome and found a higher percentage of primary reads aligned to T2T-CHM13 than to HG38 across all chromosomes. MAPQ scores further confirmed that these reads were uniquely aligned. Additionally, I performed a T-test to confirm that the HG38 and T2T-CHM13 genomes are significantly different. These findings suggest that the T2T-CHM13 genome provides more comprehensive alignment and may yield more accurate insights. Therefore, future studies should adopt the T2T-CHM13 genome as the standard, and efforts should be made to improve its annotation to increase accessibility. Additionally, high impact studies should be realigned to the T2T-CHM13 genome to determine if any new conclusions can be found. Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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